Table 2.

Summary of the SNP polymorphisms detected in the different cotton subpopulations^a

Origin	Accession No.	Accessions with phenotype data	Polymorphic SNPs	SNPs MAF > 0.05	SNPs MAF > 0.1
The Yellow River Valley	182	166	59,402	49,975	40,540
The Yangtze River Valley	79	75	59,428	55,337	46,434
Northwestern inland region	22	22	57,294	51,875	46,656
Northern specifically early maturation region	16	16	56,085	53,888	45,126
The introduced landraces	13	9	52,113	49,884	40,745
Outgroup	20	0	54,310	51,404	43,336
Total	332	288	59,502	57,071	48,940

^aMAF, minor allele frequency; SNP, single nucleotide polymorphism

Accessions with phenotype data for GWAS analysis between SNP loci and salt-tolerance related traits

Outgroup was involved in 5 wild cotton, 13 semi-wild cotton and 2 sea-island cotton materials